library(readr)
map_result <- read_table("Count_chromosomes.txt", 
                         col_names = FALSE) 
colnames(map_result) <- c("chr","Chromosome_length","Mapped_reads","Unknown")
Chromosome_to_remove = c("1","10","11","12","13","14","15","16","17","18","19","2","20","21","22","3","4","5","6","7","8","9","MT","X","Y","
                          KI270728.1","KI270727.1","KI270442.1","KI270729.1","GL000225.1","KI270743.1","GL000008.2","GL000009.2,
                          KI270747.1","KI270722.1","GL000194.1","KI270742.1","GL000205.2","GL000195.1","KI270736.1","KI270733.1","
                          GL000224.1","GL000219.1","KI270719.1","GL000216.2","KI270712.1","KI270706.1","KI270725.1","KI270744.1","
                          KI270734.1","GL000213.1","GL000220.1","KI270715.1","GL000218.1","KI270749.1","KI270741.1","GL000221.1","
                          KI270716.1","KI270731.1","KI270751.1","KI270750.1","KI270519.1","GL000214.1","KI270708.1","KI270730.1,
                          KI270438.1","KI270737.1","KI270721.1","KI270738.1","KI270748.1","KI270435.1","GL000208.1","KI270538.1,
                          KI270756.1","KI270739.1","KI270757.1","KI270709.1","KI270746.1","KI270753.1","KI270589.1","KI270726.1,
                          KI270735.1","KI270711.1","KI270745.1","KI270714.1","KI270732.1","KI270713.1","KI270754.1","KI270710.1,
                          KI270717.1","KI270724.1","KI270720.1","KI270723.1","KI270718.1","KI270317.1","KI270740.1","KI270755.1","
                          KI270707.1","KI270579.1","KI270752.1","KI270512.1","KI270322.1","GL000226.1","KI270311.1","KI270366.1,
                          KI270511.1","KI270448.1","KI270521.1","KI270581.1","KI270582.1","KI270515.1","KI270588.1","KI270591.1","
                          KI270522.1","KI270507.1","KI270590.1","KI270584.1","KI270320.1","KI270382.1","KI270468.1","KI270467.1,
                          KI270362.1","KI270517.1","KI270593.1","KI270528.1","KI270587.1","KI270364.1","KI270371.1","KI270333.1,
                          KI270374.1","KI270411.1","KI270414.1","KI270510.1","KI270390.1","KI270375.1","KI270420.1","KI270509.1,
                          KI270315.1","KI270302.1","KI270518.1","KI270530.1","KI270304.1","KI270418.1","KI270424.1","KI270417.1,
                          KI270508.1","KI270303.1","KI270381.1","KI270529.1","KI270425.1","KI270396.1","KI270363.1","KI270386.1,
                          KI270465.1","KI270383.1","KI270384.1","KI270330.1","KI270372.1","KI270548.1","KI270580.1","KI270387.1,
                          KI270391.1","KI270305.1","KI270373.1","KI270422.1","KI270316.1","KI270340.1","KI270338.1","KI270583.1,
                          KI270334.1","KI270429.1","KI270393.1","KI270516.1","KI270389.1","KI270466.1","KI270388.1","KI270544.1,
                          KI270310.1","KI270412.1","KI270395.1","KI270376.1","KI270337.1","KI270335.1","KI270378.1","KI270379.1,
                        KI270329.1","KI270419.1","KI270336.1","KI270312.1","KI270539.1","KI270385.1","KI270423.1","KI270392.1",
                         "GL000009.2","KI270394.1","GL000224.1","KI270438.1","KI270707.1","KI270717.1","KI270726.1","KI270728.1",
                         "KI270730.1","KI270734.1","KI270735.1","KI270747.1")

map_result <- map_result %>% 
  dplyr::filter(!(chr %in% Chromosome_to_remove)) %>% 
  dplyr::filter(Mapped_reads >= 50) %>% 
  dplyr::select(chr)
map_result_name <- rep(NA,length(map_result))
for (i in 1:length(map_result$chr)){
  temp <- stringr::str_replace_all(map_result$chr[i],"\\|","_")
  map_result_name[i] <- paste0(temp,".bam")
}
write_tsv(map_result,"target_chr.txt",col_names = FALSE)
write_tsv(data.frame(map = map_result_name),"target_chrname.txt",col_names = FALSE)



